rs58582188

chr10-8074288-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001002295.2(GATA3):c.*266dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00812 in 505,786 control chromosomes in the GnomAD database, including 39 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.013 (25 hom., cov: 32)
  • Exomes 𝑓: 0.0061 (14 hom.)
• Consequence: GATA3 NM_001002295.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.42

Genes affected

GATA3 (HGNC:4172): (GATA binding protein 3) This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is an important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-8074288-A-AT is Benign according to our data. Variant chr10-8074288-A-AT is described in ClinVar as [Likely_benign]. Clinvar id is 1201835.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1948/151792) while in subpopulation AFR AF= 0.0298 (1233/41386). AF 95% confidence interval is 0.0284. There are 25 homozygotes in gnomad4. There are 918 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd at 1947 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA3	NM_001002295.2	c.*266dup		3_prime_UTR_variant	6/6	ENST00000379328.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA3	ENST00000379328.9	c.*266dup		3_prime_UTR_variant	6/6	1	NM_001002295.2	A1
GATA3	ENST00000346208.4	c.*266dup		3_prime_UTR_variant	6/6	1		P4

Frequencies

GnomAD3 genomes AF: 0.0128 AC: 1947 AN: 151674 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.00780

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00208

Gnomad FIN AF: 0.00265

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00629

Gnomad OTH AF: 0.0144

GnomAD4 exome AF: 0.00610 AC: 2159 AN: 353994 Hom.: 14 Cov.: 0 AF XY: 0.00591 AC XY: 1076 AN XY: 182164

Gnomad4 AFR exome AF: 0.0250

Gnomad4 AMR exome AF: 0.0103

Gnomad4 ASJ exome AF: 0.00817

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00231

Gnomad4 FIN exome AF: 0.00297

Gnomad4 NFE exome AF: 0.00588

Gnomad4 OTH exome AF: 0.00963

GnomAD4 genome AF: 0.0128 AC: 1948 AN: 151792 Hom.: 25 Cov.: 32 AF XY: 0.0124 AC XY: 918 AN XY: 74190

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0119

Gnomad4 ASJ AF: 0.00780

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00209

Gnomad4 FIN AF: 0.00265

Gnomad4 NFE AF: 0.00630

Gnomad4 OTH AF: 0.0143

Alfa AF: 0.00168 Hom.: 1

Asia WGS AF: 0.00375 AC: 14 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 06, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs58582188; hg19: chr10-8116251;